Problem reading vcf file. #71

CanadianGPD opened this Issue Sep 4, 2012 · 3 comments


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2 participants


I'm having trouble reading my vcf file with PyVCF. Any help would be useful the file I'm trying to read was created by vcf tools.

Here is the code:

import vcf
vcf_reader = vcf.Reader(open('all.mergedSNPs.vcf','r'))
for rec in vcf_reader:
print rec

But I get this error
Traceback (most recent call last):
File "", line 1, in
File "/Library/Python/2.7/site-packages/PyVCF-0.6.0-py2.7-macosx-10.7-intel.egg/vcf/", line 443, in next
pos = int(row[1])
IndexError: list index out of range


jamescasbon commented Sep 23, 2012

Is there an extra trailing blank line in the file?


jamescasbon commented Sep 25, 2012

Can you try again with HEAD?


jamescasbon commented Dec 5, 2012

No response from OP and PR merged, closing

jamescasbon closed this Dec 5, 2012

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